In the gene analysis, an analysis method utilizing the amplification of a template nucleic acid using a primer and the detection of the amplified product or the detection of the hybridization between the obtained amplified product and a probe is used widely. In the analysis, a probe that detects the amplification reaction of a template nucleic acid, a substance that intercalates into the amplified product, a probe that generates or quenches fluorescence by hybridizing to the amplified product, and the like are used. This method can achieve, for example, the analysis of the presence or absence of a target sequence (qualitative analysis), the analysis of the quantity of the target sequence (quantitative analysis), the typing of a polymorphism site in the target sequence, and the like. The typing can determine, for example, the type of the base (for example, wild type or mutant type) of the polymorphism site, the genotype (homozygous or heterozygous), and the like.
In the gene analysis utilizing the amplification of a template nucleic acid, however, the amplification and the amplification bias of a nucleic acid sequence other than the template nucleic acid sometimes occur, which causes the problems in the specificity, the quantitativity, the sensitivity, and the like. In the medical field, there is a need to detect a small amount of template nucleic acid in a sample. Thus, there is a demand for a gene analysis method with higher accuracy.